I want to extract the sequences based on the output of *.core_sweeps.csv, which provided the start and end positions.
In the README, you mentioned that
*.core_sweeps.csv: The positions (in the coordinates of the whole genome alignment) of core genome sweeps.
I guess the align/*.core.fasta is not what you mentioned, as it was concatenated and only contains core genome. Besides, it has gap. The align/*maf seems to be the whole genome alignment, while it was not concatenated, making it hard to mapping the position. So I was wondering if the positions are in coordinates of the reference genome, which was provided in the phybreak_parameters.txt at ref_iso.
Hi,
I want to extract the sequences based on the output of
*.core_sweeps.csv, which provided the start and end positions. In theREADME, you mentioned thatI guess the
align/*.core.fastais not what you mentioned, as it was concatenated and only contains core genome. Besides, it has gap. Thealign/*mafseems to be the whole genome alignment, while it was not concatenated, making it hard to mapping the position. So I was wondering if the positions are in coordinates of the reference genome, which was provided in thephybreak_parameters.txtatref_iso.Thanks in advance!
Best, Xiaojun